In the technique of Atomic Layer Deposition a substrate is exposed sequentially and alternately to at least two mutually reactive reactants. The substrate is heated to a temperature that is high enough to prevent condensation of the reactants but low enough to prevent thermal decomposition of each of the reactants. The substrate is exposed to the first reactant and the first reactant is chemisorbed onto the surface of the substrate until the surface is occupied with a monolayer of the first reactant. Then the chemisorption saturates and excess reactant is exhausted. Then the supply of the first reactant is cut-off and the reaction chamber is evacuated and/or purged to remove the traces of non-chemisorbed first reactant from the gas phase. Then the substrate is exposed to the second reactant which reacts with the chemisorbed first reactant under the formation of a solid film and the release of gaseous reaction products until the monolayer of the first reactant has fully reacted with the second reactant and the surface of the substrate is covered with a chemisorbed monolayer of the second reactant. Then the process saturates and excess of the second reactant is exhausted. This cycle can be repeated a number of times until a sufficiently thick film has been deposited onto the substrate. More than two reactants can be used, in particular for the deposition of ternary or more complicated compounds or multilayers. This technique has been known since 1980, see the review article of Suntola, “Atomic Layer Epitaxy” in: “Handbook of Christal Growth 3, Thin Films and Epitaxy, part B: Growth Mechanisms and Dynamics,” by D. T. J. Hurle, Ed. Elsevier, 1994, Chapter 14, p 601–663. Because only a monolayer of the material is deposited per cycle, a sufficient number of cycles needs to be executed to achieve the required film thickness. In order to minimize the cycle time without compromising the effectiveness of the purging of the reactor, the volume of the reactor has been minimized and the flow dynamics of the reactor has been optimized. A first example of the reactor is given in U.S. Pat. No. 5,711,811 which is incorporated herein by reference. This patent describes a reactor in which a plurality of substrates can be processed simultaneously. In this reactor, a stack of narrowly spaced substrates is formed and the direction of the gas flow is parallel to the main surfaces of the substrates, an inlet located at one side of a substrate surface and the exhaust located at the other side of the substrate surface. Although it is an advantage that a plurality of substrates can be processed simultaneously, making the relatively slow technique more economical, it is a disadvantage that the formation of the stack of substrates needs to be carried out manually. In Finnish patent application Ser. No. 991078 of Microchemistry Oy is a single wafer reactor for Atomic Layer Deposition is described which allows robotic loading and unloading of the substrate. The disadvantage of the reactor is that only one wafer is processed at a time, using the relatively slow Atomic Layer Deposition technique. It is the object of the present invention to overcome these disadvantages and provide a method for operating the Atomic Layer Deposition technique that allows batch processing and robotic handling of the waters.